The rapid weight loss that occurs in obese patients submitted to Roux-en-y gastric bypass (RYGB) as well as the changes in dietary pattern and the intestinal malabsorption result in changes in bone mineral density (BMD). The objective of the present study was to assess the changes in BMD after the weight loss induced by RYGB using ultrasound of the phalanges and compare the results with those obtained by dual-energy X-ray absorptiometry (DXA). We conducted a 1-yr prospective longitudinal study on women with grade III obesity submitted to RYGB. Anthropometric (weight, height, body mass index, and abdominal circumference) and body composition measurements by electrical bioimpedance, assessment of food consumption by 24-h recall, biochemical evaluation, and assessment of BMD by ultrasonography of the phalanges and DXA (BMD values are from the 33% radius site) were performed during the preoperative period and 3, 6, and 12 mo after surgery. The mixed-effects linear regression model was used to analyze the effect of postoperative time on the variable of interest, and the kappa coefficient (p < 0.05) was used to compare the concordance of the methods used for BMD evaluation. Twenty-nine patients were included in the study. During the 1-yr follow-up, a reduction of 39 ± 8 kg (71 ± 15% of excess weight) and 29 ± 7 kg of fat mass was observed. Calcium and zinc concentrations were reduced after 12 mo. No difference in caffeine, calcium, or sodium consumption was observed between the preoperative and postoperative periods. Analysis of BMD by ultrasonography of the phalanges 1 yr after surgery showed increased values of amplitude-dependent speed of sound (2064.6 ± 59.4 vs 2154.7 ± 63 m/s; p < 0.001) and ultrasound bone profile index (0.73 ± 0.13 vs 0.76 ± 0.14; p < 0.001). Analysis of BMD by DXA showed a reduction of BMD values (0.6 ± 0.04 vs 0.57 ± 0.05 g/cm³; p < 0.001) in the sixth month and maintenance of the values from the sixth to the 12th month. At the end of the study, there was no concordance between the methods for BMD analysis. This study showed improvement in bone quality and quantity assessed by ultrasonography. However, the DXA results showed a reduction in BMD after 12 mo of RYGB. Thus, the BMD measurement methods were discordant.